ontology updates w/ 5.0.0

[jahilton]

• 48d354f5-a5ca-4f35-a3bb-fa3687502252 obs.var_time:P7 - update to 7 day [MmusDv:0000117]
• d86517f0-fa7e-4266-b82e-a521350d6d36
  • obs.Dataset:RomanovDev10x - update to 23 day [MmusDv:0000144]
  • obs.Dataset: Mickelsen10x - update to 4wk [MmusDv:0000149]
  • obs.Dataset: Flynn10x - update to 4wk [MmusDv:0000149]
  • obs.SRA_ID:SRR5164436 - update to juvenile [MmusDv:0000178]
  • obs.SRA_ID:SRR5164437 - update to juvenile [MmusDv:0000178]
  • obs.SRA_ID:SRR5164438 - update to 4wk [MmusDv:0000149]
• 91c8e321-566f-4f9d-b89e-3a164be654d5 - only Dataset
  • author_cell_type: L4-5IT_RORB_TSHZ2 should be CL:4030062 (L4/5 intratelencephalic projecting glutamatergic neuron)
  • author_cell_type: L2-4IT_CUX2 should be CL:4030059 (L2/3 intratelencephalic projecting glutamatergic neuron)
  • author_cell_type: L4-5IT_RORB_LRRK1 should be CL:4030062 (L4/5 intratelencephalic projecting glutamatergic neuron)
  • author_cell_type: L4-5IT_RORB_ARHGAP15 should be CL:4030062 (L4/5 intratelencephalic projecting glutamatergic neuron)
  • author_cell_type: L6IT_THEMIS_LINC00343 should be CL:4030065 (L6 intratelencephalic projecting glutamatergic neuron)
  • author_cell_type: L6IT_THEMIS_CUX1 should be CL:4030065 (L6 intratelencephalic projecting glutamatergic neuron)
  • author_cell_type: L3-5IT_RORB_PLCH1 should be CL:4030061 (L3 intratelencephalic projecting glutamatergic neuron)
• Private Collection: A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup
  • Dataset: Major cell Cluster: CNS neurons
  • CL:0003001 (bistratified retinal ganglion cell) should be CL:4033053 (small bistratified retinal ganglion cell)
  • Dataset: Major cell Cluster: Epithelial cells
  • CL:0000068 (duct epithelial cell) should be CL:4030066 (ureteric bud cell)
  • Dataset: Whole dataset: Raw counts only
  • CL:0003001 (bistratified retinal ganglion cell) should be CL:4033053 (small bistratified retinal ganglion cell)
  • CL:0000068 (duct epithelial cell) should be CL:4030066 (ureteric bud cell)

[corismall]

Private collection: Molecular and cellular evolution of the primate dorsolateral prefrontal cortex now public ID: e1fa9900-3fc9-4b57-9dce-c95724c88716

Dataset: All (only one dataset) _cell_type_ontology_termid: CL:4023040 (L2/3-6 intratelencephalic projecting glutamatergic neuron) should be CL:4030059 (L2/3 intratelencephalic projecting glutamatergic neuron)

[brian-mott]

4a9fd4d7-d870-4265-89a5-ad51ab811d89 assay_ontology_term_id will need update once this NTR resolves assay_ontology_term_id = EFO:0022490

[Jchaffer787]

03608e22-227a-4492-910b-3cb3f16f952e Dataset: All of them Need to change disease_ontology_term_id from ‘MONDO:1011336’ for ‘nervous system disorder, non-human animal’ to ‘MONDO:1010239' for ‘peripheral neuropathy, non-human animal’. Need to change assay_ontology_term_id from 'EFO:0008930' for 'Smart-seq' to ‘EFO:0022488’ for ‘Smart-seq3’

[brian-mott]

Private collection: Multiomic Profiling of Human Clonal Hematopoiesis Reveals Genotype and Cell-Specific Inflammatory Pathway Activation Dataset: all of them disease_ontology_term_id: MONDO:0060782 updated when this NTR resolves

[corismall]

Private collection: Dysregulation of brain and choroid plexus cell types in severe COVID-19 no public ID: 59c9ecfe-c47d-4a6a-bab0-895cc0c1942b Dataset: all in adata.obs['cellID2'] change cell_type_ontology_term_id for:

• L5/6 excitatory neuron to CL:4030067
• L5/6 CC excitatory neuron to CL:4030067
• L2/3 excitatory neuron to CL:4030059
• L4 excitatory neuron to CL:4030063

[jahilton]

The above notes that will need to carry on to a future migration

• 48d354f5-a5ca-4f35-a3bb-fa3687502252 obs.var_time:P7 - update to 7 day [MmusDv:0000117]
• d86517f0-fa7e-4266-b82e-a521350d6d36
  • obs.Dataset:RomanovDev10x - update to 23 day [MmusDv:0000144]
  • obs.Dataset: Mickelsen10x - update to 4wk [MmusDv:0000149]
  • obs.Dataset: Flynn10x - update to 4wk [MmusDv:0000149]
  • obs.SRA_ID:SRR5164436 - update to juvenile [MmusDv:0000178]
  • obs.SRA_ID:SRR5164437 - update to juvenile [MmusDv:0000178]
  • obs.SRA_ID:SRR5164438 - update to 4wk [MmusDv:0000149]
• Multiomic Profiling of Human Clonal Hematopoiesis Reveals Genotype and Cell-Specific Inflammatory Pathway Activation
  • disease_ontology_term_id: MONDO:0060782 updated pending https://github.com/monarch-initiative/mondo/issues/7137

[corismall]

Private collection: Mouse perinatal heart maturation scRNA-seq

• obs['age'] = P4 - update to 4 day [MmusDv:0000114]
• obs['age'] = P7 - update to 7 day [MmusDv:0000117]

[jahilton]

Migration completed. The leftovers carried into #825